Linear mixed-effects models using Eigen and S4

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Documentation for package ‘lme4’ version 1.1-6

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A B C D E F G I L M N O P Q R S T U V W X misc

lme4-package Linear, generalized linear, and nonlinear mixed models

-- A --

anova.merMod Class "merMod" of Fitted Mixed-Effect Models
as.data.frame.thpr Profile method for merMod objects
as.data.frame.VarCorr.merMod Extract Variance and Correlation Components

-- B --

bootMer Model-based (Semi-)Parametric Bootstrap for Mixed Models

-- C --

cake Breakage Angle of Chocolate Cakes
cbpp Contagious bovine pleuropneumonia
coef.merMod Class "merMod" of Fitted Mixed-Effect Models
confint.merMod Compute confidence intervals on the parameters of an lme4 fit

-- D --

densityplot.thpr Mixed-Effects Profile Plots (Regular / Density / Pairs)
devcomp Extract the deviance component list
deviance.merMod Class "merMod" of Fitted Mixed-Effect Models
dotplot.ranef.mer Extract the modes of the random effects
drop1.merMod Drop all possible single fixed-effect terms from a mixed effect model
dummy Dummy variables (experimental)
Dyestuff Yield of dyestuff by batch
Dyestuff2 Yield of dyestuff by batch

-- E --

expandDoubleVerts Expand terms with "||" notation into separate "|" terms

-- F --

findbars Determine random-effects expressions from a formula
fitted.merMod Class "merMod" of Fitted Mixed-Effect Models
fixed.effects Extract fixed-effects estimates
fixef Extract fixed-effects estimates
fixef.merMod Extract fixed-effects estimates
formula.merMod Class "merMod" of Fitted Mixed-Effect Models
fortify add information to data based on a fitted model
fortify.merMod add information to data based on a fitted model

-- G --

getL Extract or Get Generalized Components from a Fitted Mixed Effects Model
getL-method Extract or Get Generalized Components from a Fitted Mixed Effects Model
getME Extract or Get Generalized Components from a Fitted Mixed Effects Model
GHrule Univariate Gauss-Hermite quadrature rule
glFormula Modular functions for mixed model fits
glmer Fit Generalized Linear Mixed-Effects Models
glmer.nb glmer() for Negative Binomial
glmerControl Control of Mixed Model Fitting
glmerMod-class Class "merMod" of Fitted Mixed-Effect Models
glmFamily Generator object for the 'glmFamily' class
glmFamily-class Class '"glmFamily"' - a reference class for 'family'
glmResp Generator objects for the response classes
glmResp-class Classes '"lmResp"', '"glmResp"', '"nlsResp"' and '"lmerResp"'
golden Generator object for the golden search optimizer class.
golden-class Class '"golden"'
GQdk Sparse Gaussian Quadrature grid
GQN Sparse Gauss-Hermite quadrature grids
grouseticks Data on red grouse ticks from Elston et al. 2001
grouseticks_agg Data on red grouse ticks from Elston et al. 2001

-- I --

InstEval University Lecture/Instructor Evaluations by Students at ETH
isGLMM Check characteristics of models
isLMM Check characteristics of models
isNested Is f1 nested within f2?
isNLMM Check characteristics of models
isREML Check characteristics of models

-- L --

lFormula Modular functions for mixed model fits
lme4 Linear, generalized linear, and nonlinear mixed models
lmer Fit Linear Mixed-Effects Models
lmerControl Control of Mixed Model Fitting
lmerMod-class Class "merMod" of Fitted Mixed-Effect Models
lmerResp Generator objects for the response classes
lmerResp-class Classes '"lmResp"', '"glmResp"', '"nlsResp"' and '"lmerResp"'
lmList List of lm Objects with a Common Model
lmList-class Class "lmList" of 'lm' Objects on Common Model
lmResp Generator objects for the response classes
lmResp-class Classes '"lmResp"', '"glmResp"', '"nlsResp"' and '"lmerResp"'
log.thpr Profile method for merMod objects
logLik.merMod Class "merMod" of Fitted Mixed-Effect Models

-- M --

mcmcsamp Getting p-values for fitted models
merMod Class "merMod" of Fitted Mixed-Effect Models
merMod-class Class "merMod" of Fitted Mixed-Effect Models
merPredD Generator object for the 'merPredD' class
merPredD-class Class '"merPredD"' - a dense predictor reference class
mkdevfun Create a deviance evaluation function from a predictor and a response module
mkGlmerDevfun Modular functions for mixed model fits
mkLmerDevfun Modular functions for mixed model fits
mkMerMod Create a merMod object
mkRespMod Create an lmerResp, glmResp or nlsResp instance
mkReTrms Create Z, Lambda, Lind, etc.
mkVarCorr Make Variance and Correlation Matrices from 'theta'
model.frame.merMod Class "merMod" of Fitted Mixed-Effect Models
model.matrix.merMod Class "merMod" of Fitted Mixed-Effect Models
modular Modular functions for mixed model fits

-- N --

NelderMead Class '"NelderMead"' of Nelder-Mead optimizers and its Generator
NelderMead-class Class '"NelderMead"' of Nelder-Mead optimizers and its Generator
Nelder_Mead Nelder-Mead Optimization of Parameters, Possibly (Box) Constrained
ngrps Number of levels
nlformula Manipulate a nonlinear model formula.
nlmer Fit Nonlinear Mixed-Effects Models
nlmerControl Control of Mixed Model Fitting
nlmerMod-class Class "merMod" of Fitted Mixed-Effect Models
nlsResp Generator objects for the response classes
nlsResp-class Classes '"lmResp"', '"glmResp"', '"nlsResp"' and '"lmerResp"'
nobars Omit terms separated by vertical bars in a formula

-- O --

optimizeGlmer Modular functions for mixed model fits
optimizeLmer Modular functions for mixed model fits

-- P --

Pastes Paste strength by batch and cask
Penicillin Variation in penicillin testing
plot.merMod diagnostic plots for merMod fits
predict.merMod Predictions from a model at new data values
print.merMod Class "merMod" of Fitted Mixed-Effect Models
print.summary.merMod Class "merMod" of Fitted Mixed-Effect Models
profile-methods Profile method for merMod objects
profile.merMod Profile method for merMod objects
pvalues Getting p-values for fitted models

-- Q --

qqmath.ranef.mer Extract the modes of the random effects

-- R --

ranef Extract the modes of the random effects
ranef.merMod Extract the modes of the random effects
refit Refit a model with a new response, by maximum likelihood criterion
refit.merMod Refit a model with a new response, by maximum likelihood criterion
refitML Refit a model by maximum likelihood criterion
refitML.merMod Refit a model by maximum likelihood criterion
rePos Generator object for the rePos (random-effects positions) class
rePos-class Class '"rePos"'
residuals.glmResp residuals of merMod objects
residuals.lmResp residuals of merMod objects
residuals.merMod residuals of merMod objects

-- S --

show-method Class "lmList" of 'lm' Objects on Common Model
show-method Class "merMod" of Fitted Mixed-Effect Models
show.merMod Class "merMod" of Fitted Mixed-Effect Models
show.summary.merMod Class "merMod" of Fitted Mixed-Effect Models
sigma Extract residual standard error
simulate.formula Simulate responses from a 'merMod' object
simulate.merMod Simulate responses from a 'merMod' object
sleepstudy Reaction times in a sleep deprivation study
splom.thpr Mixed-Effects Profile Plots (Regular / Density / Pairs)
subbars "Sub[stitute] Bars"
summary.merMod Class "merMod" of Fitted Mixed-Effect Models
summary.summary.merMod Class "merMod" of Fitted Mixed-Effect Models

-- T --

terms.merMod Class "merMod" of Fitted Mixed-Effect Models

-- U --

update.merMod Class "merMod" of Fitted Mixed-Effect Models
updateGlmerDevfun Modular functions for mixed model fits

-- V --

VarCorr Extract Variance and Correlation Components
VarCorr.merMod Extract Variance and Correlation Components
varianceProf Transform to the variance scale
vcov.merMod Class "merMod" of Fitted Mixed-Effect Models
vcov.summary.merMod Class "merMod" of Fitted Mixed-Effect Models
VerbAgg Verbal Aggression item responses

-- W --

weights.merMod Class "merMod" of Fitted Mixed-Effect Models

-- X --

xyplot.thpr Mixed-Effects Profile Plots (Regular / Density / Pairs)

-- misc --

.makeCC Control of Mixed Model Fitting
.simulateFun Simulate responses from a 'merMod' object